Review V1 configuration and add documentation

[mattldawson]

This PR makes minor updates to the V1 configuration format in preparation for a final V1 release. It also adds documentation for V1 format. It also creates a new "development" version example that can be used for in-progress mechanism components (e.g., condensed-phase reactions), and removes all condensed-phase reactions from the V1 documentation.

Subsequent PRs will create a development parser that will contain all existing parsing logic from the V1 parser, after which, any parsing logic not required to support the V1 format in the documentation will be removed from the V1 parser.

The surface reaction was modified to remove the condensed phase. This will be re-added to the development parser once it is created.

closes #138

[github-actions]

📄 Documentation for this branch is available at: https://ncar.github.io/MechanismConfiguration/branch/develop-138-review/

[Copilot]

Pull Request Overview

This PR finalizes the V1 configuration format by removing condensed-phase reactions and adding comprehensive documentation. It prepares for the V1 release while creating a development version that maintains all existing parsing capabilities.

• Removes condensed-phase components from the V1 surface reaction configuration and parser
• Adds complete V1 documentation including reaction types, phases, species, and examples
• Creates a new development configuration that preserves all condensed-phase reaction functionality

Reviewed Changes

Copilot reviewed 47 out of 67 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
test/unit/v1/v1_unit_configs/reactions/surface/*.yaml/json	Removes condensed phase references from surface reaction test configurations
test/unit/v1/reactions/test_parse_surface.cpp	Updates surface reaction tests to remove condensed phase validation
test/integration/test_v1_parser.cpp	Updates V1 parser tests to reflect simplified configuration
test/integration/test_development_parser.cpp	Adds new test file for development parser with full feature set
src/v1/reactions/surface_parser.cpp	Removes condensed phase parsing logic from V1 surface parser
include/mechanism_configuration/v1/reaction_types.hpp	Removes condensed_phase field from Surface reaction type
examples/v1/full_configuration.yaml/json	Simplifies V1 examples to gas-phase only reactions
examples/development/full_configuration.yaml/json	Creates development examples with all reaction types
docs/source/v1/**	Adds comprehensive V1 documentation for all components

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[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.95%. Comparing base (856ebb3) to head (41815bb).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

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  Coverage   86.95%   86.95%           
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  Files           3        3           
  Lines          23       23           
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  Hits           20       20           
  Misses          3        3           

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[boulderdaze]

Looks good! Just curious, what's the reason for including the zip file in the repo? eg. docs/source/_static/examples/v1/json/chapman/chapman.zip?

[mattldawson]

Looks good! Just curious, what's the reason for including the zip file in the repo? eg. docs/source/_static/examples/v1/json/chapman/chapman.zip?

I think that's what MusicBox Interactive uses when someone tries to download an example configuration. (But, I'm not sure about that)